Genome-wide Analysis of Histone Lysine Methylation Variations Caused by Diabetic Conditions in Human Monocytes
Aberrant histone lysine methylation patterns that change chromatin structure can promote dysregulated gene transcription and disease progression. Diabetic conditions such as high glucose (HG) are known to alter key pathologic pathways. However, their impact on cellular histone lysine methylation is unknown. We hypothesized that chronic HG can induce aberrant changes in histone H3 lysine 4 and lysine 9 dimethylation (H3K4me2 and H3K9me2) within target cells. Chromatin immunoprecipitation linked to microarrays (ChIP-on-chip) is currently a widely used approach for acquiring genome-wide information on histone modifications. We adopted this approach to profile and compare the variations in H3K4me2 and H3K9me2 in human gene coding and CpG island regions in THP-1 monocytes cultured in normal glucose and HG. Subsequently, we identified key relevant candidate genes displaying differential changes in H3K4me2 and H3K9me2 in HG versus normal glucose and also validated them with follow-up conventional ChIPs. Relevance to human diabetes was demonstrated by noting that H3K9me2 at the coding and promoter regions of two candidate genes was significantly greater in blood monocytes of diabetic patients relative to normal controls similar to the THP-1 data. In addition, regular mRNA profiling with cDNA arrays revealed correlations between mRNA and H3K9me2 levels. These novel results show histone methylation variations, for the first time, under diabetic conditions at a genome-wide level. Aberrant histone lysine methylation patterns that change chromatin structure can promote dysregulated gene transcription and disease progression. Diabetic conditions such as high glucose (HG) are known to alter key pathologic pathways. However, their impact on cellular histone lysine methylation is unknown. We hypothesized that chronic HG can induce aberrant changes in histone H3 lysine 4 and lysine 9 dimethylation (H3K4me2 and H3K9me2) within target cells. Chromatin immunoprecipitation linked to microarrays (ChIP-on-chip) is currently a widely used approach for acquiring genome-wide information on histone modifications. We adopted this approach to profile and compare the variations in H3K4me2 and H3K9me2 in human gene coding and CpG island regions in THP-1 monocytes cultured in normal glucose and HG. Subsequently, we identified key relevant candidate genes displaying differential changes in H3K4me2 and H3K9me2 in HG versus normal glucose and also validated them with follow-up conventional ChIPs. Relevance to human diabetes was demonstrated by noting that H3K9me2 at the coding and promoter regions of two candidate genes was significantly greater in blood monocytes of diabetic patients relative to normal controls similar to the THP-1 data. In addition, regular mRNA profiling with cDNA arrays revealed correlations between mRNA and H3K9me2 levels. These novel results show histone methylation variations, for the first time, under diabetic conditions at a genome-wide level. Genome-wide analysis of histone lysine methylation variations caused by diabetic conditions in human monocytes.Journal of Biological ChemistryVol. 285Issue 19PreviewVOLUME 282 (2007) PAGES 13854–13863 Full-Text PDF Open Access Histone modifications in chromatin, particularly histone lysine methylation, play key roles in gene expression and are emerging as a visible new layer of gene transcription regulation (1Strahl B.D. Allis C.D. Nature. 2000; 403: 41-45Crossref PubMed Scopus (6670) Google Scholar, 2Zhang Y. Reinberg D. Genes Dev. 2001; 15: 2343-2360Crossref PubMed Scopus (1245) Google Scholar, 3Sims 3rd, R.J. Nishioka K. Reinberg D. Trends Genet. 2003; 19: 629-639Abstract Full Text Full Text PDF PubMed Scopus (540) Google Scholar). Depending upon the timing and chromosomal location, histone methylation cannot only undergo dynamic changes during gene transcription and cell division, but also remain semi-stable, well maintained, and somatically inheritable. Along with DNA methylation, histone methylation can contribute to epigenetic heritable changes in gene function that do not involve a local change in DNA sequence. It has been shown that changes in histone methylation follow specific patterns and encode information during cell cycle changes and development (4Litt M.D. Simpson M. Gaszner M. Allis C.D. Felsenfeld G. Science. 2001; 293: 2453-2455Crossref PubMed Scopus (520) Google Scholar). Therefore, aberrant alterations in histone lysine methylation patterns that change chromatin structure could lead to dysregulated gene transcription and disease progression (5Fraga M.F. Ballestar E. Villar-Garea A. Boix-Chornet M. Espada J. Schotta G. Bonaldi T. Haydon C. Ropero S. Petrie K. Iyer N.G. Perez-Rosado A. Calvo E. Lopez J.A. Cano A. Calasanz M.J. Colomer D. Piris M.A. Ahn N. Imhof A. Caldas C. Jenuwein T. Esteller M. Nat. Genet. 2005; 37: 391-400Crossref PubMed Scopus (1529) Google Scholar). Elucidating the biological and functional relevance of these post-translational histone modifications is crucial to our understanding of the role of chromatin in gene expression. To date, compared with the extensive literature available on gene mutations, there is very little data linking histone modification variations to human disease, largely due to the lack of effective identification methods. DNA microarray technology has made it possible to profile and quantify the expression of thousands of genes simultaneously (6Schena M. Shalon D. Davis R.W. Brown P.O. Science. 1995; 270: 467-470Crossref PubMed Scopus (7667) Google Scholar). Although the major use of DNA microarrays has been for mRNA expression profiling, there are other applications (7van Steensel B. Nat. 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Pergamenschikov A. Williams C.F. Jeffrey S.S. Botstein D. Brown P.O. Nat. Genet. 1999; 23: 41-46Crossref PubMed Scopus (0) Google Scholar), we recently use a array approach to profile and analyze histone lysine methylation patterns in the coding regions of human genes F. Natarajan R. Mol. Cell. Biol. 2005; 25: 4650-4661Crossref PubMed Scopus (96) Google Scholar). Although the is high the array approach can histone variations at the gene is and as little as of We this to in histone and dimethylation between and HG THP-1 cells. approach is in microarray are in data at in the human the are in the gene coding and promoter We used human cDNA and CpG island arrays to these CpG array a of the CpG in the human genome with a transcription not of promoter regions D. J. C. N. M. P. T.H. I. J.R. R. 2005; PubMed Scopus Google Scholar). the cDNA and CpG arrays used in this a but and of the human show that H3K4me2 and H3K9me2 are in regions that are and in eukaryotes K. Allis C.D. 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Biol. 2005; 25: 4650-4661Crossref PubMed Scopus (96) Google Scholar), of the candidate genes are not with candidate genes and but a very of genes can in and we that H3K4me2 and H3K9me2 are also on CpG is that the number of the H3K9me2 is greater H3K4me2 on CpG that H3K9me2 is within CpG of results for the first time, a of H3K4me2 and at gene coding and promoter regions in monocytes under and HG We analysis the in to H3K4me2 and H3K9me2 under and HG a of and we identified H3K4me2 and for and HG, and H3K9me2 and for and HG, cDNA and H3K4me2 and for and HG, and H3K9me2 and for and HG, CpG only between H3K4me2 and H3K9me2 on the cDNA and on the CpG of candidate genes are in data and Histone in THP-1 under HG we H3K4me2 and H3K9me2 candidate gene variations under versus HG Our was to genes that changes in their methylation during HG two genes that are H3K4me2 H3K9me2 that are by the only under genes that are under conditions, but show and Therefore, genes that show methylation between HG and NG, but are not identified as H3K4me2 H3K9me2 in the target Whereas these have caused genes that changes in methylation but not identified by our it the of Genes displaying differential methylation identified by applying the to the cDNA array and the results are in and H3K4me2 in HG compared with the other and H3K9me2, genes methylation under HG compared with and genes methylation methylation alterations by chronic HG Open in a new To the microarray genes that in H3K4me2 and and in H3K9me2 and by conventional We also DNA with for to that changes are specific to HG. shown in 3 and the conventional results of these and are with the array in histone methylation by these conventional also visible in the DNA microarray these the of the array data. analysis was also to the CpG differential H3K4me2, and differential is available in To the of these was to the human genome D. J. C. N. M. P. T.H. I. J.R. R. 2005; PubMed Scopus Google Scholar), and of these could to the human of these CpG island can as within within gene within the genome but not to the data several CpG variations in histone and only a of these to their promoter coding methylation alterations by chronic HG Open in a new the identified in the CpG a histone lysine to the of proteins J.R. A. F. M. S. E. E. G. M. Y. Cell. Full Text Full Text PDF PubMed Scopus Google Scholar, R.J. K. Y. D. P. J. Y. Nature. PubMed Scopus Google Scholar), a in histone H3K4me2, an in histone H3K9me2 at their promoter regions under HG conditions conventional that H3K4me2 at the promoter and H3K9me2 at the promoter are under HG conditions and is that is a 3rd, R.J. Reinberg D. Genes Dev. PubMed Scopus Google Scholar, R. C. Kouzarides T. Nat. Cell. Biol. 2004; PubMed Scopus Google that can gene expression by is a gene our novel new that HG could methylation of the a new by HG could the expression of genes by the other is a of and also has in the and A. R. R. Lee B. Y. E. Proc. Natl. Acad. Sci. U. S. A. 2004; PubMed Scopus Google Scholar). To the relevance of our at the we the mRNA expression of in THP-1 cell under versus HG conditions expression of was very in THP-1 but was by the We under HG conditions, the of relative to conditions at the promoter of for this to in THP-1 under HG an to the of HG and a role for histone H3K9me2 in expression that the of cellular histone modification in to in with monocytes in diabetic are to conditions and our with THP-1 can to human blood to disease and To the relevance to we compared histone H3K9me2 in two candidate genes the THP-1 cell data. we compared H3K9me2 in the coding and promoter regions by in blood monocytes a of diabetic patients relative to normal DNA and as F. Natarajan R. J. Biol. 2004; Full Text Full Text PDF PubMed Scopus Google the blood of patients with T1D, T2D, and normal with an DNA the monocytes of was and the conventional data in and in show that diabetic patients and have higher of histone H3K9me2 the promoter and coding regions relative to in the normal is similar to the results with THP-1 cell in controls between mRNA and H3K4me2 and of cDNA arrays for mapping histone methylation is that we can histone methylation and mRNA expression to possible We and HG and mRNA profiling versus by to cDNA arrays to compare changes in mRNA genes displaying altered histone between HG variations of histone methylation and the of mRNA expression under conditions are also in genes that a in H3K9me2, the mRNA expression of was 9 and only the candidate genes the in H3K9me2, the mRNA expression of 4 and 2 the other the on the show that the of H3K4me2 with mRNA expression is In variations in H3K9me2, but not H3K4me2, have an with gene expression. In an to examine for to the we and for analysis of their histone modification and shown in at the of histone in show changes in in to HG. gene expression is in HG H3K9me2 is with However, gene expression was H3K9me2, also in to HG. and not show changes in These results that histone modifications can to the expression of but not as also by 3rd, R.J. Nishioka K. Reinberg D. Trends Genet. 2003; 19: 629-639Abstract Full Text Full Text PDF PubMed Scopus (540) Google Scholar, Grunstein M. Nat. Scopus Google Scholar). we analysis of the histone and candidate data 4 and methylation profiling and the expression data mRNA profiling to examine the correlations between methylation and mRNA expression levels. genes with higher expression are to have higher on the mRNA profiling this for H3K4me2 and H3K9me2 candidate genes with the mRNA two data a of H3K4me2 candidate genes show high on the cDNA H3K9me2 candidate genes also high on the cDNA array that not histone H3K9me2 are in gene expression. These results are not and methylation are linked to transcription and However, our data the that histone methylation profiling data that the methylation of the chromatin, mRNA profiling data of mRNA that the of transcription and other mRNA is by several reports of and methylation Mol. Cell. 2005; 19: Full Text Full Text PDF PubMed Scopus Google Scholar, X. T. M. E. T. D. P. F. M.R. N. C. F. A. D.E. Y. J. O. Nature. PubMed Scopus Google Scholar). microarray profiling of gene histone methylation profiling data that histone methylation under a specific and a of the cell at the layer of histone It is and and such as and the types of DNA can the of this the profiling information the of histone in the the between methylation and also their variations under Our in this was to dynamic alterations in histone lysine methylation by these under and HG conditions and analyze and compare these We also a profiling with and HG DNA on the DNA array a and that it has a higher X. A. D. and R. data. We adopted the cDNA and CpG arrays that we used of human use of these arrays have in that of histone methylation changes at and their and are high However, still have key in that a of human genes at an an is that the cDNA arrays are as little as of DNA compared with for cDNA arrays particularly cell number is a mRNA profiling on cDNA we and correlations between H3K4me2, H3K9me2, and gene expression. was that not histone H3K9me2 in gene expression. It is possible that these H3K9me2 candidate genes are but by a of H3K9me2 are still in the cell that is in with our that changes in H3K9me2 with changes in gene expression biological of histone methylation at gene promoter and coding regions are still not Although that genes can at and genes are by methylation at and 3rd, R.J. Nishioka K. Reinberg D. Trends Genet. 2003; 19: 629-639Abstract Full Text Full Text PDF PubMed Scopus (540) Google Scholar), this are reported and also in our a that was in the coding regions of genes Mol. 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Natarajan R. 2003; PubMed Scopus Google Scholar). we methylation at histone J.R. A. F. M. S. E. E. G. M. Y. Cell. Full Text Full Text PDF PubMed Scopus Google Scholar, R.J. K. Y. D. P. J. Y. Nature. PubMed Scopus Google Scholar), could a novel by HG HG also altered the methylation of genes such as and that could relevant to diabetes these genes are with and pathways. in we a in at the coding and promoter regions in monocytes and in at with these in we used a and diabetes and biological networks our genes in our candidate genes in for and to and and to to and in the such as well as the functional and biological relevance of between HG, and histone methylation variations is of it could to the in the of for the and of and J. 2003; 290: PubMed Scopus Google Scholar). in H3K4me2 and H3K9me2 as this of transcription by chronic HG and key remain whether these changes in histone methylation are and are the in the to these These are by the that in diabetic We and for diabetic and of for with data We S. at of and P. of for with